ngsReports: Default FastQC Summary Report
/Users/lachlanbaer/Documents/Bioinformatics/Projects/20200310_rRNADepletion/1_trimmedData/FastQC
24 March, 2020
FastQC Summary
| Filename | Total | Flagged As Poor Quality | Sequence Length | %GC |
|---|---|---|---|---|
| ERR1698341.fastq.gz | 8,798,953 | 0 | 15-307 | 45 |
| ERR1698342.fastq.gz | 13,089,605 | 0 | 15-342 | 46 |
| ERR1698343.fastq.gz | 16,265,173 | 0 | 15-350 | 46 |
| ERR1698344.fastq.gz | 9,151,485 | 0 | 15-326 | 47 |
| ERR1698345.fastq.gz | 12,223,488 | 0 | 15-357 | 46 |
| ERR1698346.fastq.gz | 7,371,645 | 0 | 15-363 | 45 |
| ERR1698347.fastq.gz | 8,535,679 | 0 | 15-365 | 47 |
| ERR1698348.fastq.gz | 8,872,590 | 0 | 15-226 | 45 |
| ERR1698349.fastq.gz | 11,036,978 | 0 | 15-227 | 45 |
| ERR1698350.fastq.gz | 12,172,034 | 0 | 15-351 | 45 |
| ERR1698351.fastq.gz | 17,531,380 | 0 | 15-356 | 46 |
| ERR1698352.fastq.gz | 9,546,474 | 0 | 15-349 | 45 |
| ERR2206799.fastq.gz | 5,523,036 | 0 | 15-247 | 50 |
| ERR2206800.fastq.gz | 6,373,724 | 0 | 15-263 | 50 |
| ERR2206801.fastq.gz | 6,411,641 | 0 | 15-260 | 49 |
| ERR2206802.fastq.gz | 5,923,216 | 0 | 15-261 | 51 |
| ERR2206803.fastq.gz | 3,881,167 | 0 | 15-359 | 50 |
| ERR2206804.fastq.gz | 4,234,146 | 0 | 15-361 | 51 |
| ERR2206805.fastq.gz | 3,667,697 | 0 | 15-358 | 50 |
| ERR2206806.fastq.gz | 3,095,424 | 0 | 15-333 | 51 |
| ERR2206807.fastq.gz | 4,789,935 | 0 | 15-311 | 50 |
| ERR2206808.fastq.gz | 4,554,344 | 0 | 15-266 | 50 |
| ERR2206809.fastq.gz | 5,554,624 | 0 | 15-274 | 48 |
| ERR2206810.fastq.gz | 5,358,885 | 0 | 15-255 | 51 |
| SRR2138286.fastq.gz | 15,015,807 | 0 | 15-51 | 48 |
| SRR2138287.fastq.gz | 13,872,845 | 0 | 15-51 | 49 |
| SRR2138288.fastq.gz | 14,796,757 | 0 | 15-51 | 49 |
| SRR2138289.fastq.gz | 13,990,758 | 0 | 15-51 | 47 |
| SRR2138290.fastq.gz | 14,180,465 | 0 | 15-51 | 48 |
| SRR2138291.fastq.gz | 14,922,322 | 0 | 15-51 | 48 |
| SRR2138292.fastq.gz | 13,985,638 | 0 | 15-51 | 47 |
| SRR2138293.fastq.gz | 15,172,337 | 0 | 15-51 | 48 |
| SRR2138294.fastq.gz | 14,505,063 | 0 | 15-51 | 48 |
| SRR2138295.fastq.gz | 14,401,651 | 0 | 15-51 | 47 |
| SRR2180293.fastq.gz | 23,373,422 | 0 | 15-50 | 52 |
| SRR2180294.fastq.gz | 22,783,161 | 0 | 15-50 | 43 |
| SRR2180295.fastq.gz | 17,259,017 | 0 | 15-50 | 48 |
| SRR2180296.fastq.gz | 22,768,006 | 0 | 15-50 | 54 |
| SRR2180297.fastq.gz | 18,409,683 | 0 | 15-50 | 45 |
| SRR2180298.fastq.gz | 26,120,718 | 0 | 15-50 | 43 |
| SRR2180299.fastq.gz | 20,521,248 | 0 | 15-50 | 44 |
| SRR2180300.fastq.gz | 17,998,453 | 0 | 15-50 | 45 |
Read Totals
Library Sizes ranged between 3,095,424 and 26,120,718 reads.
Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.
FastQC Summary
Summary of FastQC flags for each parameter
Per Base Sequence Quality
Heatmap showing mean base qualities for each library
Per Sequence Quality Scores
Heatmap showing mean sequence qualities for each library
Per Base Sequence Content
Heatmap of summed base distributions along each read
Per Sequence GC Content
GC Content Heatmap normalised to theoretical GC content in the Hsapiens Transcriptome
GC Content Distributions for all reads showing theoretical GC content from the Hsapiens Transcriptome
Sequence Length Distribution
Sequence Duplication Levels
Adapter Content
Universal Adapter Content
Overrepresented Summary
Total overrepresented sequences for each library
Overrepresented Sequences
## Overrepresented_sequences missing from ERR1698341.fastq.gz## Overrepresented_sequences missing from ERR1698342.fastq.gz## Overrepresented_sequences missing from ERR1698343.fastq.gz## Overrepresented_sequences missing from ERR1698344.fastq.gz## Overrepresented_sequences missing from ERR1698345.fastq.gz## Overrepresented_sequences missing from ERR1698346.fastq.gz## Overrepresented_sequences missing from ERR1698347.fastq.gz## Overrepresented_sequences missing from ERR1698348.fastq.gz## Overrepresented_sequences missing from ERR1698349.fastq.gz## Overrepresented_sequences missing from ERR1698350.fastq.gz## Overrepresented_sequences missing from ERR1698351.fastq.gz## Overrepresented_sequences missing from ERR1698352.fastq.gz## Overrepresented_sequences missing from ERR2206799.fastq.gz## Overrepresented_sequences missing from ERR2206800.fastq.gz## Overrepresented_sequences missing from ERR2206801.fastq.gz## Overrepresented_sequences missing from ERR2206803.fastq.gz## Overrepresented_sequences missing from ERR2206804.fastq.gz## Overrepresented_sequences missing from ERR2206805.fastq.gz## Overrepresented_sequences missing from ERR2206806.fastq.gz## Overrepresented_sequences missing from ERR2206807.fastq.gz## Overrepresented_sequences missing from ERR2206808.fastq.gz## Overrepresented_sequences missing from ERR2206809.fastq.gz## Overrepresented_sequences missing from ERR2206810.fastq.gz## Overrepresented_sequences missing from SRR2180294.fastq.gz## Overrepresented_sequences missing from SRR2180297.fastq.gz## Overrepresented_sequences missing from SRR2180300.fastq.gz| Sequence | Total | Present In | Overall Percentage | Max_Percentage | Possible_Source |
|---|---|---|---|---|---|
| AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | 284,500 | 10 | 0% | 0.223143% | No Hit |
| CCTCACGGTACTTGTCCGCTATCGGTCTCGTGCCGGTATTTAGCCTT | 241,626 | 10 | 0% | 0.189642% | No Hit |
| GGGAGTTTGACTGGGGCGGTACACCTGTCAAACGGTAACGCAGGTGTCCT | 214,960 | 3 | 0% | 0.435448% | No Hit |
| GTTGGATTGTTCACCCACTAATAGGGAACGTGAGCTGGGTTTAGACCGTC | 192,588 | 3 | 0% | 0.464841% | No Hit |
| CTTCGATGTCGGCTCTTCCTATCATTGTGAAGCAGAATTCACCAAGCGTT | 184,681 | 3 | 0% | 0.404853% | No Hit |
| GCCCTGTTGAACTCTCTCTTCAAAGTTCTTTTCAACTTTCCCTCACGGTAC | 163,176 | 9 | 0% | 0.136463% | No Hit |
| CCGGTATTTAGCCTTAGATGGAGTTTACCACCCGCTTTGGGCTGCATTCCC | 156,009 | 9 | 0% | 0.132140% | No Hit |
| GCCCTCCGTACGCCACAGGTCCCTCGCCCTCGGCAGAGGGGCGGGGATTCG | 132,563 | 8 | 0% | 0.119030% | No Hit |
| GTCGGCTCTTCCTATCATTGTGAAGCAGAATTCACCAAGCGTTGGATTGT | 121,713 | 3 | 0% | 0.228576% | No Hit |
| GTCGCTTTTTGATCCTTCGATGTCGGCTCTTCCTATCATTGTGAAGC | 120,027 | 3 | 0% | 0.252178% | No Hit |
| GGCGTACGGAAGACCCGCTCCCCGGCGCCGCTCGTGGGGGGCCCAAGTCC | 113,334 | 3 | 0% | 0.212091% | No Hit |
| GCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAATGAAGCGCGGGTAA | 113,256 | 3 | 0% | 0.239516% | No Hit |
| GGGGAGTTTGACTGGGGCGGTACACCTGTCAAACGGTAACGCAGGTGTCC | 91,046 | 3 | 0% | 0.189801% | No Hit |
| CCTAAGGCGAGCTCAGGGAGGACAGAAACCTCCCGT | 89,058 | 2 | 0% | 0.217656% | No Hit |
| GGCGGAGATGGGCGCCGCGAGGCGTCCAGTGCGGTAACGCGACCGATCCC | 79,455 | 2 | 0% | 0.186990% | No Hit |
| GTTTTAAGCAGGAGGTGTCAGAAAAGTTACCACAGGGATAACTGGCTTGT | 75,156 | 2 | 0% | 0.164793% | No Hit |
| GCTGGGTTTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTGATGATG | 74,286 | 2 | 0% | 0.184843% | No Hit |
| GTCCTAAGGCGAGCTCAGGGAGGACAGAAACCTCCCGT | 60,972 | 2 | 0% | 0.146412% | No Hit |
| CTCTGATCGTTTTTTCACTGACCCGGTGAGGCGGGGGGGCGAGCCCCG | 60,591 | 2 | 0% | 0.154981% | No Hit |
| GCTTGATCTTGATTTTCAGTACGAATACAGACCGTGAAAGCGGGGCCTC | 60,591 | 2 | 0% | 0.142292% | No Hit |
| GTGGCGGCCAAGCGTTCATAGCGACGTCGCTTTTTGATCCTTCGATGTCG | 60,503 | 2 | 0% | 0.134417% | No Hit |
| GCCGAAACGATCTCAACCTATTCTCAAACTTTAAATGGGTAAGAAGCCCG | 58,746 | 2 | 0% | 0.137913% | No Hit |
| GCCGAAGTGGAGAAGGCTTCCATGTGAACAGCAGTTGAACATGGGTCAGT | 58,511 | 2 | 0% | 0.127675% | No Hit |
| GGGTAAACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCCAAATGCCTC | 57,735 | 2 | 0% | 0.127517% | No Hit |
| GTTGTTGCCATGGTAATCCTGCTCAGTACGAGAGGAACCGCAGGTTC | 57,362 | 2 | 0% | 0.129562% | No Hit |
| CTGATGATGTGTTGTTGCCATGGTAATCCTGCTCAGTACGAGAGGAACCG | 55,708 | 2 | 0% | 0.133481% | No Hit |
| TGATGATGTGTTGTTGCCATGGTAATCCTGCTCAGTACGAGAGGAACCGC | 54,436 | 2 | 0% | 0.133714% | No Hit |
| GTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGCGCTACACTGACTG | 54,226 | 2 | 0% | 0.129924% | No Hit |
| GTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATT | 53,376 | 2 | 0% | 0.116659% | No Hit |
| AGCAAATATTCAAACGAGAACTTTGAAGGCCGAAGTGGAGAAGGCTTCC | 51,573 | 2 | 0% | 0.122922% | No Hit |
Session Information
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
locale: en_AU.UTF-8||en_AU.UTF-8||en_AU.UTF-8||C||en_AU.UTF-8||en_AU.UTF-8
attached base packages: parallel, stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: readr(v.1.3.1), stringr(v.1.4.0), magrittr(v.1.5), scales(v.1.1.0), pander(v.0.6.3), kableExtra(v.1.1.0), dplyr(v.0.8.5), ngsReports(v.1.2.0), tibble(v.2.1.3), ggplot2(v.3.3.0) and BiocGenerics(v.0.32.0)
loaded via a namespace (and not attached): bitops(v.1.0-6), matrixStats(v.0.56.0), lubridate(v.1.7.4), webshot(v.0.5.2), RColorBrewer(v.1.1-2), httr(v.1.4.1), GenomeInfoDb(v.1.22.0), tools(v.3.6.1), R6(v.2.4.1), lazyeval(v.0.2.2), colorspace(v.1.4-1), withr(v.2.1.2), tidyselect(v.1.0.0), compiler(v.3.6.1), rvest(v.0.3.5), Biobase(v.2.46.0), Cairo(v.1.5-11), flashClust(v.1.01-2), xml2(v.1.2.5), DelayedArray(v.0.12.2), plotly(v.4.9.2), ggdendro(v.0.1-20), labeling(v.0.3), digest(v.0.6.25), Rsamtools(v.2.2.3), rmarkdown(v.2.1), XVector(v.0.26.0), jpeg(v.0.1-8.1), pkgconfig(v.2.0.3), htmltools(v.0.4.0), FactoMineR(v.2.3), highr(v.0.8), htmlwidgets(v.1.5.1), rlang(v.0.4.5), rstudioapi(v.0.11), farver(v.2.0.3), zoo(v.1.8-7), hwriter(v.1.3.2), jsonlite(v.1.6.1), crosstalk(v.1.1.0.1), BiocParallel(v.1.20.1), RCurl(v.1.98-1.1), GenomeInfoDbData(v.1.2.2), leaps(v.3.1), Matrix(v.1.2-18), Rcpp(v.1.0.4), munsell(v.0.5.0), S4Vectors(v.0.24.3), lifecycle(v.0.2.0), scatterplot3d(v.0.3-41), stringi(v.1.4.6), yaml(v.2.2.1), MASS(v.7.3-51.5), SummarizedExperiment(v.1.16.1), zlibbioc(v.1.32.0), plyr(v.1.8.6), grid(v.3.6.1), ggrepel(v.0.8.2), crayon(v.1.3.4), lattice(v.0.20-40), Biostrings(v.2.54.0), hms(v.0.5.3), knitr(v.1.28), pillar(v.1.4.3), GenomicRanges(v.1.38.0), reshape2(v.1.4.3), stats4(v.3.6.1), glue(v.1.3.2), evaluate(v.0.14), ShortRead(v.1.44.3), latticeExtra(v.0.6-29), data.table(v.1.12.8), vctrs(v.0.2.4), png(v.0.1-7), gtable(v.0.3.0), purrr(v.0.3.3), tidyr(v.1.0.2), assertthat(v.0.2.1), xfun(v.0.12), viridisLite(v.0.3.0), truncnorm(v.1.0-8), GenomicAlignments(v.1.22.1), IRanges(v.2.20.2), cluster(v.2.1.0) and ellipsis(v.0.3.0)